The Drug Related Gene Database (DRG), funded by National Institute of Drug Abuse (NIDA) ARRA Supplement #HHSN27120080035C, was created to facilitate discovery and use of resources relevant to drug abuse research. The database and associated tools were specifically created for providing data that is contained in tables, figures and supplementary materials from published papers in a way that facilitates search across the results of these studies. These data are extracted from published journal articles that directly test hypotheses relevant to the neuroscience of addiction and addictive behavior. The current database mainly focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data types include the effects of a particular drug, strain, or knock out on a particular gene, in a particular anatomical region. Once loaded, these data are available for query through the NIF interface. During this process, the content is standardized using a generic high level description of a relevant study and terms are mapped to ontologies available through the NIF project (NIFSTD) to enhance semantic search of such data.

Stability of Probe IDs:

Microarray manufacturers were individually questioned about the stability of their probe ids - if they change over time. For your information, below we have their individual replies:

Illumina: "The probes ID is an unique internal Illumina reference and can change between chip versions."

and "Just to clarify, "PROBE_ID" is a unique probe identifier in the Illumina manufacturing database that distinguishes a probe across all products and all species. This should be consistent from chip to chip and if you see the same probe on different versions of a manifest, the probe sequence would be the same."

techsupport@illumina.com

NimbleGen:

"Probe IDs are linked to the design name. If the name is the same, then so are the probe IDs."

and

"The PROBE_IDs within an NDF file are fixed and do not change. So long as the design name (or better yet, the DESIGN_ID) is the same then the PROBE_ID should be stable provided the end user didn't manually edit anything."

"It is worth pointing out that there is no guarantee that PROBE_ID will be unique within a design file. It is always best to HASH on the union of CONTAINER|GENE_EXPR_OPTION, SEQ_ID, and PROBE_ID if you want to insure uniqueness."

biochemts.us@roche.com

Affymetrix: "The probe ids do not change over time."

"The sequences that they interrogate may change over time because more genes get discovered, and others may change depending on the validation by the scientific community. The changes for the sequences will be reflected in the annotation updates. The annotation updates are released three times yearly in mid-March, July and November for all arrays. If there is an update in the genome assembly build for a given organism, that update usually is reflected in the following annotation."

"Annotation updates incorporate current releases from GenBank, RefSeq, Ensembl, UniGene, Entrez Gene, UniProt and UCSC, as well as sequences from other organism-specific databases. The sources for each annotation update since release 20 are documented and available on the NetAffx Support Materials Page." support@affymetrix.com